One of the common challenges in protein-protein docking is dealing with an overwhelming number of incorrect binding predictions. These false positives can distract from promising candidates and add time-consuming work for researchers manually evaluating results. Fortunately, Hex for SAMSON offers a way to intentionally restrict the search space via range angles, helping modelers focus the docking on the most plausible binding orientations.
In this post, we’ll explore how defining receptor and ligand range angles in SAMSON’s Hex Extension allows you to limit the docking search area to known or expected interaction regions. This approach makes docking faster and filtering results easier—especially useful when you already have information about potential binding sites or interface residues.
What are Range Angles?
When docking two protein structures using Hex, the algorithm searches through thousands of ligand orientations around a fixed receptor, looking for low-energy binding conformations. By default, this sampling is carried out over the entire surface of both proteins—rotationally symmetrical across a full 180° sphere.
However, if you’re confident about the binding site or relative orientation of the binding partners, there’s no need to expend computational effort on the entire search space. This is where range angles become useful. You can define a spherical cone (with an axis that connects the centers of the receptor and ligand) which limits the angular search space to a specific portion of the protein surface.
How to Use Range Angles in SAMSON
To set this up in SAMSON with hex:
- Go to Home > Apps > Biology > Hex to open the Hex docking interface.
- In the Sampling method dropdown, choose Range angles.
- Click on Advanced parameters.
- Adjust the Receptor angle range and Ligand angle range to a smaller value—typically 45°—if you know the receptor’s binding site and the ligand’s likely orientation.
Visually, you will see two cones—one on each protein—showing the constrained search region. This can be a good sanity check to verify that the docking will be targeted correctly.
Want to go a step further? By using the Move editors, you can manually orient the ligand closer to the suspected binding site before limiting the sampling with range angles. This is especially helpful if you’re trying to reproduce an experimental result or dock homologous structures.
Why it Matters
Restricting the angular search significantly reduces:
- The number of false positives
- The time to return meaningful results
- The computational load for your docking runs
This is particularly beneficial when working with large proteins, especially in screenings or when docking known binding partners with only minor conformational changes expected.
To learn more about protein docking in SAMSON using Hex, visit the full tutorial documentation here: https://documentation.samson-connect.net/tutorials/hex/protein-docking-with-hex/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.